I was going to ask why the machines do not kill everyone who is woken from the Matrix, below we are shown a scene where Neo is woken from the Matrix,
They potentially have the power to keep things in check purely by killing anyone who wakes from the Matrix. I am not talking about being flushed down a sewer to drown and possibly be saved by a passing ship, I mean having the machine lop that persons head off right there and then. And since they have destroyed Zion several times and just left several people alive to reset the cycle all over again, no-one would be left in Zion if the machines so desired.
I understand that the computers need an anomaly to reset the matrix and restore balance. But why the need to wake "The One" from the Matrix. Couldn't the machines have achieved the same result within the Matrix by simply showing Neo what he could do indirectly with a "Program" design to teach "The One" how to do all the cool stuff he does and to have other "Programs" to rebel against the machines like Morpheous and the others do. This would serve the same purpose of getting the one to make a choice when he is the meet the Architect without the need to go in and out of the Matrix.
This way they would have full control and be able reset the cycle with minimal effort.